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Sodium in PDB 3ird: Structure of Dihydrodipicolinate Synthase From Clostridium Botulinum

Enzymatic activity of Structure of Dihydrodipicolinate Synthase From Clostridium Botulinum

All present enzymatic activity of Structure of Dihydrodipicolinate Synthase From Clostridium Botulinum:
4.2.1.52;

Protein crystallography data

The structure of Structure of Dihydrodipicolinate Synthase From Clostridium Botulinum, PDB code: 3ird was solved by R.C.J.Dobson, S.Atkinson, M.A.Perugini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.20 / 2.23
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.810, 92.810, 60.350, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 20.9

Other elements in 3ird:

The structure of Structure of Dihydrodipicolinate Synthase From Clostridium Botulinum also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Dihydrodipicolinate Synthase From Clostridium Botulinum (pdb code 3ird). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Dihydrodipicolinate Synthase From Clostridium Botulinum, PDB code: 3ird:

Sodium binding site 1 out of 1 in 3ird

Go back to Sodium Binding Sites List in 3ird
Sodium binding site 1 out of 1 in the Structure of Dihydrodipicolinate Synthase From Clostridium Botulinum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Dihydrodipicolinate Synthase From Clostridium Botulinum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:19.1
occ:1.00
 O A:ILE158 2.3 13.9 1.0
O A:HOH363 2.3 18.8 1.0
O A:ASP155 2.3 14.1 1.0
O A:HOH402 2.3 20.1 1.0
O A:CYS153 2.4 16.7 1.0
C A:ILE158 3.3 13.2 1.0
C A:CYS153 3.4 17.5 1.0
C A:ASP155 3.5 14.5 1.0
O A:HOH446 4.0 25.5 1.0
C A:GLU154 4.1 16.4 1.0
CA A:CYS153 4.1 17.5 1.0
N A:ASP155 4.1 15.2 1.0
N A:ILE158 4.2 13.4 1.0
CA A:ILE158 4.2 13.4 1.0
O A:LYS181 4.2 14.6 1.0
N A:VAL159 4.2 13.1 1.0
O A:GLU154 4.3 16.6 1.0
O A:LYS156 4.3 13.4 1.0
CA A:VAL159 4.3 11.7 1.0
CA A:ASP155 4.4 15.1 1.0
N A:GLU154 4.4 17.6 1.0
C A:LYS156 4.4 14.5 1.0
N A:LYS156 4.4 15.2 1.0
CG1 A:VAL159 4.5 11.8 1.0
CA A:GLU154 4.6 17.6 1.0
CB A:ILE158 4.6 13.8 1.0
CA A:LYS156 4.6 15.4 1.0
O A:LEU152 4.7 14.7 1.0
CB A:CYS153 4.8 17.4 1.0
C A:ASN157 4.8 13.4 1.0
N A:ASN157 4.9 13.7 1.0
CB A:ASP155 5.0 14.7 1.0

Reference:

S.Atkinson, R.C.J.Dobson, M.A.Perugini. Structure of Cbot-Dhdps To Be Published.
Page generated: Mon Oct 7 11:01:31 2024

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